Managing Flatpak permissions and file storage outside of the flatpak can be difficult to manage. Flatseal fixes all that!
flatpak install flathub com.github.tchx84.Flatseal
View each flatpak permissions
See user modified permissions
Reset permissions in the top right corner
The thing I use the most is filesystem access. This lets you specify the flatpak can read from other parts in the filesystem.
This is the best way to manage and maintain flatpaks with ease and it’s the first thing I install after the base flatpak!